# Deep copy warning -- efficient coding?

**URL:** <https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048>\
**Category:** Modeling\
**Created:** [October 16, 2018, 6:44pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048 "2018-10-16T18:44:44Z")\
**Posts on this page:** 11\
**Page:** 1

<div class="post-metadata">

**Author:** ![Charles\_Driver](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charles_driver/32/6524_2.png) [@Charles\_Driver](https://discourse.mc-stan.org/u/Charles_Driver)\
**Post date:** [October 16, 2018, 6:44pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/1 "2018-10-16T18:44:44Z")

</div>

If I am constructing a symmetric matrix S, typically I have done something like  
S[i,j] = complex operation  
s[j,i] = s[i,j]

with stan 2.18 this approach generates a lot of warnings. What is the preferred way to approach this?

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 16, 2018, 7:01pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/2 "2018-10-16T19:01:39Z")

</div>

I think `s[j,i] = s[i,j]` does not actually trigger a warning, but other things do. The most common way to avoid them is to use `foo += bar;` rather than `foo = foo + bar;`. Unfortunately, the `Info` does not print out the filename or line number, but you can probably figure out where they are.

```
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=o) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=o) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=o) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=o) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=l) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=DRDI) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=cz1) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=cz0) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=out) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=out) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=covm) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=l) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=l) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=counter) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=counter) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sMANIFESTVAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sT0VAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=state) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=state) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ypredcov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ypredcov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=merrorstates) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfstates) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sMANIFESTVAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=sT0VAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=etacov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=discreteDIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=eta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=state) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=state) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ypredcov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ypredcov) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=merrorstates) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfmeasures) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=ukfstates) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=pop_DIFFUSION) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=pop_MANIFESTVAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=pop_T0VAR) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=popsd) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

```

---

<div class="post-metadata">

**Author:** ![Charles\_Driver](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charles_driver/32/6524_2.png) [@Charles\_Driver](https://discourse.mc-stan.org/u/Charles_Driver)\
**Post date:** [October 16, 2018, 7:13pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/3 "2018-10-16T19:13:55Z")

</div>

Thanks, I’m aware of the += and am happy to be able to use that in more cases with 2.18, but still this function generates 4 warnings:

```
sm <- '
functions{
matrix covsqrt2corsqrt(matrix mat, int invert){ 
        matrix[rows(mat),cols(mat)] o;
        vector[rows(mat)] s;
        o=mat;
      
        for(i in 1:rows(o)){ //set upper tri to lower
          for(j in min(i+1,rows(mat)):rows(mat)){
            o[j,i] = inv_logit(o[j,i])*2-1; 
            o[i,j] = o[j,i];
          }
          o[i,i]=1;
        }
      
        if(invert==1) o = inverse(o);
      
        for(i in 1:rows(o)){
          s[i] = inv_sqrt(o[i,] * o[,i]);
          if(is_inf(s[i])) s[i]=0;
        }
        o= diag_pre_multiply(s,o);
        return o;
}
}
model{
}'

s <- stan_model(model_code = sm)
```

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 16, 2018, 7:32pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/4 "2018-10-16T19:32:28Z")

</div>

I think that comes from `if(invert==1) o = inverse(o);` and `o= diag_pre_multiply(s,o);` rather than `o[i,j] = o[j,i];`

---

<div class="post-metadata">

**Author:** ![Charles\_Driver](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charles_driver/32/6524_2.png) [@Charles\_Driver](https://discourse.mc-stan.org/u/Charles_Driver)\
**Post date:** [October 16, 2018, 7:39pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/5 "2018-10-16T19:39:30Z")

</div>

That would only generate two warnings by my count, but regardless, the general question still stands – is an operation like:

```
o = inverse(o)

```

actually inefficient, and if so, how should one handle this situation?

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 16, 2018, 7:41pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/6 "2018-10-16T19:41:48Z")

</div>

I think all of the ways to handle that would also involve a copy, although some might avoid the message. You could do something like

```
if (invert) {
  matrix[rows(o), cols(o)] o_inv = inverse(o);
  ... 
}
```

---

<div class="post-metadata">

**Author:** ![Charles\_Driver](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charles_driver/32/6524_2.png) [@Charles\_Driver](https://discourse.mc-stan.org/u/Charles_Driver)\
**Post date:** [October 16, 2018, 8:01pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/7 "2018-10-16T20:01:11Z")

</div>

Ok. It’s nice that such information is available, but it’s not so nice when it generates a page of spurious warnings that (I think?) can’t be disabled. Also, `o[i,j] = o[j,i];` does generate the warning.

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 16, 2018, 8:08pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/8 "2018-10-16T20:08:52Z")

</div>

They can’t be disabled but they can be avoided. In the loop, maybe try

```
real tmp = whatever;
o[i,j] = tmp;
o[j,i] = tmp;

```

---

<div class="post-metadata">

**Author:** ![Charles\_Driver](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/charles_driver/32/6524_2.png) [@Charles\_Driver](https://discourse.mc-stan.org/u/Charles_Driver)\
**Post date:** [October 16, 2018, 8:17pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/9 "2018-10-16T20:17:23Z")

</div>

Ok, and that should be of equal or greater efficiency? Seems like an extra operation to my naive thinking.

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 16, 2018, 8:17pm UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/10 "2018-10-16T20:17:52Z")

</div>

Same efficiency, less warnings about the lack of efficiency.

---

<div class="post-metadata">

**Author:** ![mitzimorris](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mitzimorris/32/29_2.png) [@mitzimorris](https://discourse.mc-stan.org/u/mitzimorris)\
**Post date:** [October 23, 2018, 4:09am UTC](https://discourse.mc-stan.org/t/deep-copy-warning-efficient-coding/6048/11 "2018-10-23T04:09:39Z")

</div>

this is parser bug - [https://github.com/stan-dev/stan/issues/2677](https://github.com/stan-dev/stan/issues/2677)